SearchParameters (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.identification_parameters.SearchParameters

All Implemented Interfaces:

MarshallableParameter, Serializable
```
public class SearchParameters
extends Object
implements Serializable, MarshallableParameter
```
This class groups the parameters used for identification.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SearchParameters.MassAccuracyType
Possible mass accuracy types.
- Nested classes/interfaces inherited from interface com.compomics.util.preferences.MarshallableParameter
  MarshallableParameter.Type

Nested Classes
Modifier and Type	Class and Description
`static class`	`SearchParameters.MassAccuracyType` Possible mass accuracy types.

Constructor Summary

Constructors
Constructor and Description

SearchParameters()
Constructor.

SearchParameters(SearchParameters searchParameters)
Constructor.

Constructors
Constructor and Description
`SearchParameters()` Constructor.
`SearchParameters(SearchParameters searchParameters)` Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(SearchParameters otherSearchParameters)` Returns true if the search parameter objects have identical settings.
`Set<Integer>`	`getAlgorithms()` Returns the algorithms for which specific parameters are stored.
`HashMap<Integer,IdentificationAlgorithmParameter>`	`getAlgorithmSpecificParameters()` Returns the algorithm specific parameters in a map: algorithm as indexed in the Advocate class > parameters.
`Enzyme`	`getEnzyme()` Returns the enzyme used for digestion.
`File`	`getFastaFile()` Returns the sequence database file used for identification.
`static String[]`	`getForwardIons()` Returns the list of forward ions.
`HashMap<String,no.uib.jsparklines.data.XYDataPoint>`	`getFractionMolecularWeightRanges()` Returns the user provided molecular weight ranges for the fractions.
`SearchParameters.MassAccuracyType`	`getFragmentAccuracyType()` Returns the fragment accuracy type.
`Double`	`getFragmentIonAccuracy()` Returns the MS2 ion m/z tolerance.
`Double`	`getFragmentIonAccuracyInDaltons(Double refMass)` Returns the absolute fragment ion tolerance in Dalton.
`IdentificationAlgorithmParameter`	`getIdentificationAlgorithmParameter(int algorithmID)` Returns the algorithm specific parameters, null if not found.
`static SearchParameters`	`getIdentificationParameters(File searchParametersFile)` Loads the identification parameters from a file.
`static String[]`	`getIons()` Getter for the list of ion symbols used.
`Integer`	`getIonSearched1()` Getter for the first kind of ion searched.
`Integer`	`getIonSearched2()` Getter for the second kind of ion searched.
`Charge`	`getMaxChargeSearched()` Returns the maximal charge searched.
`Integer`	`getMaxIsotopicCorrection()` Returns the maximal isotopic correction.
`Charge`	`getMinChargeSearched()` Returns the minimal charge searched.
`Integer`	`getMinIsotopicCorrection()` Returns the minimal isotopic correction.
`Integer`	`getnMissedCleavages()` Returns the allowed number of missed cleavages.
`Double`	`getPrecursorAccuracy()` Returns the precursor tolerance.
`Double`	`getPrecursorAccuracyDalton()` Returns the precursor tolerance in Dalton (for de novo searches).
`SearchParameters.MassAccuracyType`	`getPrecursorAccuracyType()` Returns the precursor accuracy type.
`PtmSettings`	`getPtmSettings()` Returns the PTM settings.
`static String[]`	`getRewindIons()` Returns the list of rewind ions.
`String`	`getShortDescription()` Returns a short description of the parameters.
`MarshallableParameter.Type`	`getType()` Returns the type of marshalled parameter from an unmarshalled object.
`Boolean`	`isPrecursorAccuracyTypePpm()` Returns true if the current precursor accuracy type is ppm.
`static void`	`saveIdentificationParameters(SearchParameters searchParameters, File searchParametersFile)` Saves the identification parameters to a serialized file.
`void`	`saveIdentificationParametersAsTextFile(File file)` Saves the identification parameters as a human readable text file.
`void`	`setDefaultAdvancedSettings()` Set the advanced settings to the default values.
`void`	`setDefaultAdvancedSettings(SearchParameters searchParameters)` Set the advanced settings to the values in the given search parameters object or to the default values of the advanced settings are not set for a given advocate.
`void`	`setEnzyme(Enzyme enzyme)` Sets the enzyme used for digestion.
`void`	`setFastaFile(File fastaFile)` Sets the sequence database file used for identification.
`void`	`setFractionMolecularWeightRanges(HashMap<String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges)` Set the user provided molecular weight ranges for the fractions.
`void`	`setFragmentAccuracyType(SearchParameters.MassAccuracyType fragmentAccuracyType)` Sets the fragment accuracy type.
`void`	`setFragmentIonAccuracy(Double fragmentIonMZTolerance)` Sets the fragment ion m/z tolerance.
`void`	`setIdentificationAlgorithmParameter(int algorithmID, IdentificationAlgorithmParameter identificationAlgorithmParameter)` Adds identification algorithm specific parameters.
`void`	`setIonSearched1(String ionSearched1)` Setter for the first kind of ion searched, indexed by its single letter code, for example "a".
`void`	`setIonSearched2(String ionSearched2)` Setter for the second kind of ion searched, indexed by its single letter code, for example "a".
`void`	`setMaxChargeSearched(Charge maxChargeSearched)` Sets the maximal charge searched.
`void`	`setMaxIsotopicCorrection(Integer maxIsotopicCorrection)` Sets the maximal isotopic correction.
`void`	`setMinChargeSearched(Charge minChargeSearched)` Sets the minimal charge searched.
`void`	`setMinIsotopicCorrection(Integer minIsotopicCorrection)` Sets the minimal isotopic correction.
`void`	`setnMissedCleavages(Integer nMissedCleavages)` Sets the allowed number of missed cleavages.
`void`	`setPrecursorAccuracy(Double precursorTolerance)` Sets the precursor tolerance.
`void`	`setPrecursorAccuracyDalton(Double precursorToleranceDalton)` Sets the precursor tolerance in Dalton (for de novo searches).
`void`	`setPrecursorAccuracyType(SearchParameters.MassAccuracyType precursorAccuracyType)` Sets the precursor accuracy type.
`void`	`setPtmSettings(PtmSettings ptmSettings)` Sets the PTM settings.
`void`	`setType()` Sets the parameters type.
`String`	`toString()`
`String`	`toString(boolean html)` Returns the search parameters as a string.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - SearchParameters
```
public SearchParameters()
```
    Constructor.
  - SearchParameters
```
public SearchParameters(SearchParameters searchParameters)
```
    Constructor.
    
    Parameters:
    
    searchParameters - the search parameter to base the search parameters on.
- Method Detail
  - setDefaultAdvancedSettings
```
public void setDefaultAdvancedSettings()
```
    Set the advanced settings to the default values.
  - setDefaultAdvancedSettings
```
public void setDefaultAdvancedSettings(SearchParameters searchParameters)
```
    Set the advanced settings to the values in the given search parameters object or to the default values of the advanced settings are not set for a given advocate.
    
    Parameters:
    
    searchParameters - the search parameter to extract the advanced settings from
  - getPtmSettings
```
public PtmSettings getPtmSettings()
```
    Returns the PTM settings.
    
    Returns:
    
    the PTM settings
  - setPtmSettings
```
public void setPtmSettings(PtmSettings ptmSettings)
```
    Sets the PTM settings.
    
    Parameters:
    
    ptmSettings - the PTM settings
  - getFragmentIonAccuracy
```
public Double getFragmentIonAccuracy()
```
    Returns the MS2 ion m/z tolerance.
    
    Returns:
    
    the MS2 ion m/z tolerance
  - getFragmentIonAccuracyInDaltons
```
public Double getFragmentIonAccuracyInDaltons(Double refMass)
```
    Returns the absolute fragment ion tolerance in Dalton. If the tolerance is in ppm, the given reference mass is used.
    
    Parameters:
    
    refMass - the reference mass to use for the conversion of tolerances in ppm.
    
    Returns:
    
    the absolute fragment ion tolerance in Dalton
  - setFragmentIonAccuracy
```
public void setFragmentIonAccuracy(Double fragmentIonMZTolerance)
```
    Sets the fragment ion m/z tolerance.
    
    Parameters:
    
    fragmentIonMZTolerance - the fragment ion m/z tolerance
  - getEnzyme
```
public Enzyme getEnzyme()
```
    Returns the enzyme used for digestion.
    
    Returns:
    
    the enzyme used for digestion
  - setEnzyme
```
public void setEnzyme(Enzyme enzyme)
```
    Sets the enzyme used for digestion.
    
    Parameters:
    
    enzyme - the enzyme used for digestion
  - getFastaFile
```
public File getFastaFile()
```
    Returns the sequence database file used for identification.
    
    Returns:
    
    the sequence database file used for identification
  - setFastaFile
```
public void setFastaFile(File fastaFile)
```
    Sets the sequence database file used for identification.
    
    Parameters:
    
    fastaFile - the sequence database file used for identification
  - getnMissedCleavages
```
public Integer getnMissedCleavages()
```
    Returns the allowed number of missed cleavages.
    
    Returns:
    
    the allowed number of missed cleavages
  - setnMissedCleavages
```
public void setnMissedCleavages(Integer nMissedCleavages)
```
    Sets the allowed number of missed cleavages.
    
    Parameters:
    
    nMissedCleavages - the allowed number of missed cleavages
  - getIonSearched1
```
public Integer getIonSearched1()
```
    Getter for the first kind of ion searched.
    
    Returns:
    
    the first kind of ion searched as an integer (see static fields of the PeptideFragmentIon class)
  - setIonSearched1
```
public void setIonSearched1(String ionSearched1)
```
    Setter for the first kind of ion searched, indexed by its single letter code, for example "a".
    
    Parameters:
    
    ionSearched1 - the first kind of ion searched
  - getIonSearched2
```
public Integer getIonSearched2()
```
    Getter for the second kind of ion searched.
    
    Returns:
    
    the second kind of ion searched as an integer (see static fields of the PeptideFragmentIon class)
  - setIonSearched2
```
public void setIonSearched2(String ionSearched2)
```
    Setter for the second kind of ion searched, indexed by its single letter code, for example "a".
    
    Parameters:
    
    ionSearched2 - the second kind of ion searched
  - getIons
```
public static String[] getIons()
```
    Getter for the list of ion symbols used.
    
    Returns:
    
    the list of ion symbols used
  - getForwardIons
```
public static String[] getForwardIons()
```
    Returns the list of forward ions.
    
    Returns:
    
    the forwardIons
  - getRewindIons
```
public static String[] getRewindIons()
```
    Returns the list of rewind ions.
    
    Returns:
    
    the rewindIons
  - getPrecursorAccuracy
```
public Double getPrecursorAccuracy()
```
    Returns the precursor tolerance.
    
    Returns:
    
    the precursor tolerance
  - setPrecursorAccuracy
```
public void setPrecursorAccuracy(Double precursorTolerance)
```
    Sets the precursor tolerance.
    
    Parameters:
    
    precursorTolerance - the precursor tolerance
  - getPrecursorAccuracyDalton
```
public Double getPrecursorAccuracyDalton()
```
    Returns the precursor tolerance in Dalton (for de novo searches).
    
    Returns:
    
    the precursor tolerance
  - setPrecursorAccuracyDalton
```
public void setPrecursorAccuracyDalton(Double precursorToleranceDalton)
```
    Sets the precursor tolerance in Dalton (for de novo searches).
    
    Parameters:
    
    precursorToleranceDalton - the precursor tolerance
  - getPrecursorAccuracyType
```
public SearchParameters.MassAccuracyType getPrecursorAccuracyType()
```
    Returns the precursor accuracy type.
    
    Returns:
    
    the precursor accuracy type
  - setPrecursorAccuracyType
```
public void setPrecursorAccuracyType(SearchParameters.MassAccuracyType precursorAccuracyType)
```
    Sets the precursor accuracy type.
    
    Parameters:
    
    precursorAccuracyType - the precursor accuracy type
  - getFragmentAccuracyType
```
public SearchParameters.MassAccuracyType getFragmentAccuracyType()
```
    Returns the fragment accuracy type.
    
    Returns:
    
    the fragment accuracy type
  - setFragmentAccuracyType
```
public void setFragmentAccuracyType(SearchParameters.MassAccuracyType fragmentAccuracyType)
```
    Sets the fragment accuracy type.
    
    Parameters:
    
    fragmentAccuracyType - the fragment accuracy type
  - isPrecursorAccuracyTypePpm
```
public Boolean isPrecursorAccuracyTypePpm()
```
    Returns true if the current precursor accuracy type is ppm.
    
    Returns:
    
    true if the current precursor accuracy type is ppm
  - getFractionMolecularWeightRanges
```
public HashMap<String,no.uib.jsparklines.data.XYDataPoint> getFractionMolecularWeightRanges()
```
    Returns the user provided molecular weight ranges for the fractions. The key is the fraction file path.
    
    Returns:
    
    the user provided molecular weight ranges of the fractions
  - setFractionMolecularWeightRanges
```
public void setFractionMolecularWeightRanges(HashMap<String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges)
```
    Set the user provided molecular weight ranges for the fractions. The key is the fraction file path.
    
    Parameters:
    
    fractionMolecularWeightRanges - the fractionMolecularWeightRanges to set
  - getMaxChargeSearched
```
public Charge getMaxChargeSearched()
```
    Returns the maximal charge searched.
    
    Returns:
    
    the maximal charge searched
  - setMaxChargeSearched
```
public void setMaxChargeSearched(Charge maxChargeSearched)
```
    Sets the maximal charge searched.
    
    Parameters:
    
    maxChargeSearched - the maximal charge searched
  - getMinChargeSearched
```
public Charge getMinChargeSearched()
```
    Returns the minimal charge searched.
    
    Returns:
    
    the minimal charge searched
  - setMinChargeSearched
```
public void setMinChargeSearched(Charge minChargeSearched)
```
    Sets the minimal charge searched.
    
    Parameters:
    
    minChargeSearched - the minimal charge searched
  - getAlgorithmSpecificParameters
```
public HashMap<Integer,IdentificationAlgorithmParameter> getAlgorithmSpecificParameters()
```
    Returns the algorithm specific parameters in a map: algorithm as indexed in the Advocate class > parameters. null if not set.
    
    Returns:
    
    the algorithm specific parameters in a map
  - getIdentificationAlgorithmParameter
```
public IdentificationAlgorithmParameter getIdentificationAlgorithmParameter(int algorithmID)
```
    Returns the algorithm specific parameters, null if not found.
    
    Parameters:
    
    algorithmID - the index of the search engine as indexed in the Advocate class
    
    Returns:
    
    the algorithm specific parameters
  - setIdentificationAlgorithmParameter
```
public void setIdentificationAlgorithmParameter(int algorithmID,
                                                IdentificationAlgorithmParameter identificationAlgorithmParameter)
```
    Adds identification algorithm specific parameters.
    
    Parameters:
    
    algorithmID - the algorithm id as indexed in the Advocate class
    
    identificationAlgorithmParameter - the specific parameters
  - getAlgorithms
```
public Set<Integer> getAlgorithms()
```
    Returns the algorithms for which specific parameters are stored. Warning: this does not mean that the algorithm was actually used.
    
    Returns:
    
    the algorithms for which specific parameters are stored in a set of indexes as listed in the Advocate class
  - getMinIsotopicCorrection
```
public Integer getMinIsotopicCorrection()
```
    Returns the minimal isotopic correction.
    
    Returns:
    
    the minimal isotopic correction
  - setMinIsotopicCorrection
```
public void setMinIsotopicCorrection(Integer minIsotopicCorrection)
```
    Sets the minimal isotopic correction.
    
    Parameters:
    
    minIsotopicCorrection - the minimal isotopic correction
  - getMaxIsotopicCorrection
```
public Integer getMaxIsotopicCorrection()
```
    Returns the maximal isotopic correction.
    
    Returns:
    
    the maximal isotopic correction
  - setMaxIsotopicCorrection
```
public void setMaxIsotopicCorrection(Integer maxIsotopicCorrection)
```
    Sets the maximal isotopic correction.
    
    Parameters:
    
    maxIsotopicCorrection - the maximal isotopic correction
  - getIdentificationParameters
```
public static SearchParameters getIdentificationParameters(File searchParametersFile)
                                                    throws IOException,
                                                           ClassNotFoundException
```
    Loads the identification parameters from a file. If the file is an identification parameters file, the search parameters are extracted.
    
    Parameters:
    
    searchParametersFile - the search parameter file
    
    Returns:
    
    the search parameters
    
    Throws:
    
    IOException - if an IOException occurs
    
    ClassNotFoundException - if a ClassNotFoundException occurs
  - saveIdentificationParameters
```
public static void saveIdentificationParameters(SearchParameters searchParameters,
                                                File searchParametersFile)
                                         throws IOException
```
    Saves the identification parameters to a serialized file.
    
    Parameters:
    
    searchParameters - the identification parameters
    
    searchParametersFile - the file
    
    Throws:
    
    IOException - if an IOException occurs
  - saveIdentificationParametersAsTextFile
```
public void saveIdentificationParametersAsTextFile(File file)
                                            throws IOException
```
    Saves the identification parameters as a human readable text file.
    
    Parameters:
    
    file - the file
    
    Throws:
    
    IOException - if an IOException occurs
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - getShortDescription
```
public String getShortDescription()
```
    Returns a short description of the parameters.
    
    Returns:
    
    a short description of the parameters
  - toString
```
public String toString(boolean html)
```
    Returns the search parameters as a string.
    
    Parameters:
    
    html - use HTML formatting
    
    Returns:
    
    the search parameters as a string
  - equals
```
public boolean equals(SearchParameters otherSearchParameters)
```
    Returns true if the search parameter objects have identical settings.
    
    Parameters:
    
    otherSearchParameters - the parameters to compare to
    
    Returns:
    
    true if the search parameter objects have identical settings
  - setType
```
public void setType()
```
    Description copied from interface: MarshallableParameter
    
    Sets the parameters type. The type must be set before writing a file but not in the constructor.
    
    Specified by:
    
    setType in interface MarshallableParameter
  - getType
```
public MarshallableParameter.Type getType()
```
    Description copied from interface: MarshallableParameter
    
    Returns the type of marshalled parameter from an unmarshalled object. The type must be written in the file but not set in the constructor. Null if not a MarshallableParameter.
    
    Specified by:
    
    getType in interface MarshallableParameter
    
    Returns:
    
    the type of marshalled parameter from an unmarshalled object

Class SearchParameters

Nested Class Summary

Nested classes/interfaces inherited from interface com.compomics.util.preferences.MarshallableParameter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SearchParameters

SearchParameters

Method Detail

setDefaultAdvancedSettings

setDefaultAdvancedSettings

getPtmSettings

setPtmSettings

getFragmentIonAccuracy

getFragmentIonAccuracyInDaltons

setFragmentIonAccuracy

getEnzyme

setEnzyme

getFastaFile

setFastaFile

getnMissedCleavages

setnMissedCleavages

getIonSearched1

setIonSearched1

getIonSearched2

setIonSearched2

getIons

getForwardIons

getRewindIons

getPrecursorAccuracy

setPrecursorAccuracy

getPrecursorAccuracyDalton

setPrecursorAccuracyDalton

getPrecursorAccuracyType

setPrecursorAccuracyType

getFragmentAccuracyType

setFragmentAccuracyType

isPrecursorAccuracyTypePpm

getFractionMolecularWeightRanges

setFractionMolecularWeightRanges

getMaxChargeSearched

setMaxChargeSearched

getMinChargeSearched

setMinChargeSearched

getAlgorithmSpecificParameters

getIdentificationAlgorithmParameter

setIdentificationAlgorithmParameter

getAlgorithms

getMinIsotopicCorrection

setMinIsotopicCorrection

getMaxIsotopicCorrection

setMaxIsotopicCorrection

getIdentificationParameters

saveIdentificationParameters

saveIdentificationParametersAsTextFile

toString

getShortDescription

toString

equals

setType

getType